• Asian-Australasian Journal of Animal Sciences
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• v.14 no.6
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• pp.880-884
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• 2001

Rumen microbiology research has undergone several evolutionary steps: the isolation and nutritional characterization of readily cultivated microbes; followed by the cloning and sequence analysis of individual genes relevant to key digestive processes; through to the use of small subunit ribosomal RNA (SSU rRNA) sequences for a cultivation-independent examination of microbial diversity. Our knowledge of rumen microbiology has expanded as a result, but the translation of this information into productive alterations of ruminal function has been rather limited. For instance, the cloning and characterization of cellulase genes in Escherichia coli has yielded some valuable information about this complex enzyme system in ruminal bacteria. SSU rRNA analyses have also confirmed that a considerable amount of the microbial diversity in the rumen is not represented in existing culture collections. However, we still have little idea of whether the key, and potentially rate-limiting, gene products and (or) microbial interactions have been identified. Technologies allowing high throughput nucleotide and protein sequence analysis have led to the emergence of two new fields of investigation, genomics and proteomics. Both disciplines can be further subdivided into functional and comparative lines of investigation. The massive accumulation of microbial DNA and protein sequence data, including complete genome sequences, is revolutionizing the way we examine microbial physiology and diversity. We describe here some examples of our use of genomics- and proteomics-based methods, to analyze the cellulase system of Ruminococcus flavefaciens FD-1 and explore the genome of Ruminococcus albus 8. At Illinois, we are using bacterial artificial chromosome (BAC) vectors to create libraries containing large (>75 kbases), contiguous segments of DNA from R. flavefaciens FD-1. Considering that every bacterium is not a candidate for whole genome sequencing, BAC libraries offer an attractive, alternative method to perform physical and functional analyses of a bacterium's genome. Our first plan is to use these BAC clones to determine whether or not cellulases and accessory genes in R. flavefaciens exist in clusters of orthologous genes (COGs). Proteomics is also being used to complement the BAC library/DNA sequencing approach. Proteins differentially expressed in response to carbon source are being identified by 2-D SDS-PAGE, followed by in-gel-digests and peptide mass mapping by MALDI-TOF Mass Spectrometry, as well as peptide sequencing by Edman degradation. At Ohio State, we have used a combination of functional proteomics, mutational analysis and differential display RT-PCR to obtain evidence suggesting that in addition to a cellulosome-like mechanism, R. albus 8 possesses other mechanisms for adhesion to plant surfaces. Genome walking on either side of these differentially expressed transcripts has also resulted in two interesting observations: i) a relatively large number of genes with no matches in the current databases and; ii) the identification of genes with a high level of sequence identity to those identified, until now, in the archaebacteria. Genomics and proteomics will also accelerate our understanding of microbial interactions, and allow a greater degree of in situ analyses in the future. The challenge is to utilize genomics and proteomics to improve our fundamental understanding of microbial physiology, diversity and ecology, and overcome constraints to ruminal function.

• Asian-Australasian Journal of Animal Sciences
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• v.10 no.6
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• pp.665-670
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• 1997

The digestibility (apparent) of P and other nutrients from the RSM, SBM and 2 batches of maize, wheat and barley was investigated in two experiments with 24 castrated male growing pigs. The effect of supplemental microbial phytase (1,000 U/kg) was also evaluated. The diets contained 25% RSM (Exp. 1) or 40% SBM (Exp. 2) and had no inorganic P. In each period of digestive trial, after 9 days of adaptation, faeces were collected for 5 days. The digestibility of P contained in the RSM and SBM was calculated by difference method. The P digestibility in maize, wheat, barley was on average 20, 34 and 36%, respectively. The digestibility of P in the RSM and SBM estimated from maize-based diets were 19 and 24 %, respectively. Kind of cereal grain had significant (p < 0.05) influence on the digestibility of P which was lower in the diets based on maize than wheat or barley. The digestibility of P significantly increased with the supplemental microbial phytase (on an average of 17%). Moreover, inclusion of enzyme into the diets positively affected digestibility of other nutrients, namely the protein and organic matter.

• Korean Journal of Agricultural Science
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• v.50 no.4
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• pp.841-860
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• 2023

The present study was conducted to evaluate the effects of dietary mangosteen peel extract (MPE) on growth performance, serum biochemistry, jejunum morphology, and cytokine levels in growing pigs raised at a high stocking density. A total of 120 male growing pigs (43.68 ± 0.48 kg) were randomly arranged in a 2 × 2 factorial design with stocking density (high; HD, 0.55 m²/pig and normal; ND, 0.82 m²/pig) and dietary MPE (0 or 5 g/kg) as factors. Each treatment had six replicates with four or six pigs per treatment. Feed and water were provided ad libitum for 6 weeks. The HD group exhibited lower final body weight, average daily gain, and average daily feed than the ND group (p < 0.05). None of the factors affected villus height to crypt depth ratio. Dietary MPE, but not stocking density, increased IL-10 levels in the serum com-pared to the non-supplemented control diet (p < 0.05). In the microbiome analysis, alpha diversity analysis showed significant reductions in the MPE-treated group only under normal density conditions. High density stress induced gut microbiome changes and these response was differ between normal and MPE diet fed pigs. Overall, each group exhibited different major microbial composition in the gut. In conclusion, there were significant changes in the major microbial composition in response to high-density stress, and this variation was influenced by dietary treatment.

• Microbiology and Biotechnology Letters
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• v.47 no.4
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• pp.473-486
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• 2019

In the aquatic environment, microorganisms are predominantly organized as biofilms. Biofilms are formed by the aggregation of microbial cells and are surrounded by a matrix of extracellular polymeric substances (EPS) secreted by the microbial cells. Biofilms are attached to various surfaces, such as the living tissues, indwelling medical devices, and piping of the industrial potable water system. Biofilms formed from a single species has been extensively studied. However, there is an increased research focus on multispecies biofilms in recent years. It is important to assess the microbial mechanisms underlying the regulation of multispecies biofilm formation to determine the drinking water microbial composition. These mechanisms contribute to the predominance of the best-adapted species in an aquatic environment. This review focuses on the interactions in the multispecies biofilms, such as coaggregation, co-metabolism, cross-species protection, jamming of quorum sensing, lateral gene transfer, synergism, and antagonism. Further, this review explores the dynamics and the factors favoring biofilm formation and pathogen transmission within the drinking water distribution systems. The understanding of the physiology and biodiversity of microbial species in the biofilm may aid in the development of novel biofilm control and drinking water disinfection processes.

• Korean Journal of Veterinary Research
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• v.56 no.2
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• pp.57-66
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• 2016

The gut epithelial barrier, which is composed of the mucosal layer and the intestinal epithelium, has multiple defense mechanisms and interconnected regulatory mechanisms against enteric microbial pathogens. However, many bacterial pathogens have highly evolved infectious stratagems that manipulate mucin production, epithelial cell-cell junctions, cell death, and cell turnover to promote their replication and pathogenicity in the gut epithelial barrier. In this review, we focus on current knowledge about how bacterial pathogens regulate mucin levels to circumvent the epithelial mucus barrier and target cell-cell junctions to invade deeper tissues and increase their colonization. We also describe how bacterial pathogens manipulate various modes of epithelial cell death to facilitate bacterial dissemination and virulence effects. Finally, we discuss recent investigating how bacterial pathogens regulate epithelial cell turnover and intestinal stem cell populations to modulate intestinal epithelium homeostasis.

• The Korean Journal of Food & Health Convergence
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• v.10 no.3
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• pp.19-22
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• 2024

The field of synthetic biology has emerged in response to the ongoing progress in the life sciences. Advances have been made in medicine, farming, eating, making materials, and more. Synthetic biology is the exploration of using living organisms to create new organisms. By manipulating specific genes to express targeted proteins, proteins can be created that are both productive and cost-effective. Solid-phase extraction (SPE) and liquid-liquid extraction (LLE) are employed for protein separation during the production process involving microorganisms. This study centers on Scanning Probe Microscopy (SPM) to showcase its utility in the food industry and food management. SPE is predominantly utilized as a pretreatment method to eliminate impurities from samples. In comparison to LLE, this method presents benefits such as decreased time and labor requirements, streamlined solvent extraction, automation capabilities, and compatibility with various other analytical instruments. Anion exchange chromatography (AEC) utilizes a similar methodology. Pharmaceutical companies utilize these technologies to improve the purity of biopharmaceuticals, thereby guaranteeing their quality. Used in the food and beverage industry to test chemical properties of raw materials and finished products. This exemplifies the potential of these technologies to enhance industrial development and broaden the scope of applications in synthetic biology.

• The Korean Journal of Food & Health Convergence
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• v.10 no.2
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• pp.13-17
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• 2024

Oxygen is necessary to sustain life, but reactive oxygen species (ROS) produced by oxygen metabolism can cause mutations and toxicity. ROS can damage cellular macromolecules, leading to oxidative stress, which can accelerate cell death and aging. ROS generated in food affect the taste, color, and aroma of food, and high levels of ROS in meat can cause spoilage. Superoxide dismutase (SOD) plays an important role in scavenging ROS in food and reducing their toxicity to organisms. SOD exerts its antioxidant effect by catalyzing the breakdown of O₂-• to H₂O₂. As a natural antioxidant, SOD has the ability to regenerate and maintain its activity over a long period of time without depletion, unlike chemical antioxidants that may have side effects or stability issues. This antioxidant effect of SOD has great potential in a variety of industries, and in the food industry it can be utilized to improve product quality and provide safe and healthy products to consumers. By disrupting the SOD2 and SOD3 genes in Candida albicans, we studied the effects of SOD2 and SOD3 genes on the antioxidant system, suggesting its potential as a natural antioxidant.

• Journal of Microbiology and Biotechnology
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• v.26 no.5
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• pp.883-890
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• 2016

Marine sediments are a microbial biosphere with an unknown physiology, and the sediments harbor numerous distinct phylogenetic lineages of Bacteria and Archaea that are at present uncultured. In this study, the structure of the archaeal and bacterial communities was investigated in the surface and subsurface sediments of Jeju Island using a next-generation sequencing method. The microbial communities in the surface sediments were distinct from those in the subsurface sediments; the relative abundance of sequences for Thaumarchaeota, Actinobacteria, Bacteroides, Alphaproteobacteria, and Gammaproteobacteria were higher in the surface than subsurface sediments, whereas the sequences for Euryarchaeota, Acidobacteria, Firmicutes, and Deltaproteobacteria were relatively more abundant in the subsurface than surface sediments. This study presents detailed characterization of the spatial distribution of benthic microbial communities of Jeju Island and provides fundamental information on the potential interactions mediated by microorganisms with the different biogeochemical cycles in coastal sediments.

• Journal of Physiology & Pathology in Korean Medicine
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• v.29 no.1
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• pp.101-113
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• 2015

Application of herbal medicines as natural preservatives has been increased because of its low toxicity or side effect, compared to artificial preservatives. In this study, papers and patents researching anti-microbial activity of herbal medicine were collected and analyzed by the year of publishment, species of bacteria, fungi, or yeasts, and herbal medicines used. After early 2000's, the number of paper publishment has been decreased, while that of patent registration has been increased up to early 2010's. Most studied species were Staphylococcus aureus, Bacillus subtilis, Escherichia coli and Pseudomonas aeruginosa, as gram-positive or gram-negative bacteria, and Candida albicans and Aspergillus niger as fungi. The bark of Cinnamomum cassia (L.) J. Presl was most frequently studies herbal medicine, followed by the roots of Scutellaria baicalensis Georgi and Sophora flavescens Ait. This study demonstrates that herbal medicines can be used as natural preservatives against diverse species of bacteria, fungi, or yeasts with their wide-ranged anti-microbial activities.

• Korean Journal of Microbiology
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• v.46 no.1
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• pp.1-8
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• 2010

New technologies are providing unprecedented knowledge into microbial community structure and functions. Even though nucleic acid based approaches provide a lot of information, metaproteomics could provide a high-resolution representation of genotypic and phenotypic traits of distinct microbial communities. Analyzing the metagenome from different microbial ecosystems, metaproteomics has been applied to seawater, human guts, activated sludge, acid mine drainage biofilm, and soil. Although these studies employed different approaches, they elucidated that metaproteomics could provide a link among microbial community structure, function, physiology, interaction, ecology, and evolution. These approaches are reviewed here to help gain insights into the function of microbial community in ecosystems.